Finally figured out how to overlay one indicator over another on the lower window. You have to drop the indicator on the top chart first. So if you want to add an EMA to the KST below, just drop the EMA on the main chart first. Then, right click the EMA anywhere on the chart and select Merge Down. It will drop down on top of the indicator window then.
Looks like you can also take any lower window indicator and move it up top right on top of the candles as well SG. Just select the lower indicator and Merge Up. It'll drop it right on top of the price action.